SAXSdb — 8weo

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Fragilysin

Bacteroides fragilis

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 220–405	Not recorded	NB243 × 1 ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；293 K；0.2 M Ammonium sulfate, 0.1 M Sodium acetate trihydrate pH 4.6, 25% w/v Polyethylene glycol 4,000	Resolution 1.50 Å R-free 0.197
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 220–405	Not recorded	NB243 × 1 ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；293 K；0.2 M Ammonium sulfate, 0.1 M Sodium acetate trihydrate pH 4.6, 25% w/v Polyethylene glycol 4,000	Resolution 1.50 Å R-free 0.197

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 8WEO	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
8H3X Bacteroide Fragilis Toxin in complex with nanobody 282 Deposited 2022-10-09	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 9–405（397 aa）	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.2 M Potassium thiocyanate, 20 % w/v PEG 3350	Resolution 1.66 Å R-free 0.216
8H3Y Bacteroide Fragilis Toxin in complex with nanobody 327 Deposited 2022-10-09	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 9–405（397 aa）	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.2 M Ammonium tartrate dibasic, 20% w/v Polyethylene glycol 3350, pH 6.6	Resolution 2.25 Å R-free 0.244
8H3Y Bacteroide Fragilis Toxin in complex with nanobody 327 Deposited 2022-10-09	Different construct Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 9–405（397 aa）	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.2 M Ammonium tartrate dibasic, 20% w/v Polyethylene glycol 3350, pH 6.6	Resolution 2.25 Å R-free 0.244
8H3Y Bacteroide Fragilis Toxin in complex with nanobody 327 Deposited 2022-10-09	Different construct Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 9–405（397 aa）	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.2 M Ammonium tartrate dibasic, 20% w/v Polyethylene glycol 3350, pH 6.6	Resolution 2.25 Å R-free 0.244
8WEM Bacteroides fragilis toxin 1 Deposited 2023-09-18	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 9–405（397 aa）	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.2 M Sodium malonate pH 5.0, 20% w/v Polyethylene glycol 3350, 32 mg mL-1	Resolution 1.80 Å R-free 0.202
8WEM Bacteroides fragilis toxin 1 Deposited 2023-09-18	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 9–405（397 aa）	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.2 M Sodium malonate pH 5.0, 20% w/v Polyethylene glycol 3350, 32 mg mL-1	Resolution 1.80 Å R-free 0.202
9XVH Crystal structure of mature Bacteroides fragilis toxin 1 Deposited 2025-11-26	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 220–405（186 aa）	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；Crystals were grown from a crystallization solution containing 0.2 M sodium acetate trihydrate, 0.1 M sodium cacodylate pH 6.5 and 21% (w/v) PEG 8000. The protein solution was at a concentration of 20 mg/ml.	Resolution 1.94 Å R-free 0.266
9XVH Crystal structure of mature Bacteroides fragilis toxin 1 Deposited 2025-11-26	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 220–405（186 aa）	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；Crystals were grown from a crystallization solution containing 0.2 M sodium acetate trihydrate, 0.1 M sodium cacodylate pH 6.5 and 21% (w/v) PEG 8000. The protein solution was at a concentration of 20 mg/ml.	Resolution 1.94 Å R-free 0.266
9XVH Crystal structure of mature Bacteroides fragilis toxin 1 Deposited 2025-11-26	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 220–405（186 aa）	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；Crystals were grown from a crystallization solution containing 0.2 M sodium acetate trihydrate, 0.1 M sodium cacodylate pH 6.5 and 21% (w/v) PEG 8000. The protein solution was at a concentration of 20 mg/ml.	Resolution 1.94 Å R-free 0.266
9XVH Crystal structure of mature Bacteroides fragilis toxin 1 Deposited 2025-11-26	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 220–405（186 aa）	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；Crystals were grown from a crystallization solution containing 0.2 M sodium acetate trihydrate, 0.1 M sodium cacodylate pH 6.5 and 21% (w/v) PEG 8000. The protein solution was at a concentration of 20 mg/ml.	Resolution 1.94 Å R-free 0.266

4 other PDB entries and 10 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	ENTM_BACFG
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–186； UniProt 220–405 Author chain B； PDBConstruct 1–186； UniProt 220–405

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	8weo
Deposition date deposition_date	2023-09-18
Structure title title	Bacteroides fragilis toxin in complex with neutralization nanobody
Keywords keywords	Bacteroides fragilis toxin, BFT, Nanobody, TOXIN/IMMUNE SYSTEM, TOXIN-IMMUNE SYSTEM complex; TOXIN/IMMUNE SYSTEM
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	29.53 Å
Radius of gyration Rg (electron density) rg_electron	28.76 Å
Forward intensity I(0) i0	81267400.00
Molecular weight molecular_weight	68542.0 kDa
Excluded volume excluded_volume	84464 Å³
Envelope volume envelope_volume	105120 Å³
Hydration-shell volume shell_volume	31039 Å³
Envelope diameter envelope_diameter	106.5 Å
Shell Rg shell_rg	35.43 Å
Envelope Rg envelope_rg	28.92 Å
Shape Rg shape_rg	28.80 Å
Total Rg total_rg	29.25 Å
Total atoms total_atoms	4824
Residues n_residues	618
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	100.1 Å
Rg (real space) rg_real	29.51 Å
Rg uncertainty (real space) rg_real_error	0.78 Å
I(0) (real space) i0_real	8.1270e+07
I(0) uncertainty (real space) i0_real_error	1.2920e+06
Rg (reciprocal space) rg_reciprocal	29.52 Å
I(0) (reciprocal space) i0_reciprocal	81270000.0000
Solution quality estimate total_estimate	0.8912
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	38.9 Å
Skewness Skewness skewness	0.273
Kurtosis Kurtosis kurtosis	-0.423
Angular range angular_range	— – 0.2700 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	14310000.0000
Real-space data points n_real_points	55
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.869; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.980; Smooth: 0.992

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Fragilysin
Molecular weight formula_weight	20699.0 kDa
EC 编号 ec_number	3.4.24.74
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,A
Atom count atom_count	5713

AVPSEPKTVYVICLRENGSTIYPNEVSAQMQDAANSVYAVHGLKRYVNFHFVLYTTEYSCPSGDAKEGLEGFTASLKSNPKAEGYDDQIYFLIRWGTWDNKILGMSWFNSYNVNTASDFEASGMSTTQLMYPGVMAHELGHILGAEHTDNSKDLMYATFTGYLSHLSEKNMDIIAKNLGWEAADGD

来源 Source

来源生物 organism	Bacteroides fragilis
NCBI Class编号 ncbi_taxonomy_id	817
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	NB243
Molecular weight formula_weight	14013.3 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,D

QVQLQESGGGLVQAGGSLRLSCVASGIIESINTFGWYRQAPGKQRELVADISRWGSTNYADSVRDRFTISRDNAKTTLYLQMNSLKPEDTAVYYCHAETIGYESGAHDYWGQGTQVTVSSHHHHHH

来源 Source

来源生物 organism	Vicugna pacos
NCBI Class编号 ncbi_taxonomy_id	30538
宿主生物 host_organism	Escherichia coli

Entity 3 Entity 3 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	865

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8. Citations (1)

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Unit-cell length a length_a	121.678 Å
Unit-cell length b length_b	121.678 Å
Unit-cell length c length_c	84.143 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 65
Space-group number int_tables_number	170
Crystal system crystal_system	—

Resolution resolution	1.500 Å
Low-resolution limit resolution_low	30.420 Å
R factor r_factor	0.1717
R_work r_work	0.1712
R_free r_free	0.1967

fit	/app/data/saxs_computation/we/8weo/8weo.fit
pddf	/app/data/pr_computation/we/8weo/8weo.pr.out
profile	/app/data/saxs_computation/we/8weo/8weo.dat

Bacteroides fragilis toxin in complex with neutralization nanobody

1. Protein Identity and Related Structures Protein Identity & Related Structures

Fragilysin

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)